I'll keep it simple.
Transportation : very simple with 7 day link pass (our only mistake was confusing the subway stops Harvard Ave. and Harvard...big difference :))
Lodging : Back Bay Hotel was excellent. Exceptionally clean and classy. Only draw back was no in-room coffee. They did give free bottled water though, which was nice. Location was good too.
Touristy stuff : We mainly did the Freedom Trail and just explored the different neighborhoods. A 'con' to the Freedom Trail was admission into 3 or 4 of the sites. Prudential Center/Copley Place Mall was very nice, especially if you want to get in out of the sun, or rain. North End was cool to walk around. One of our favorite spots (we have a 2 yr old) was Public Garden. Lines for the swan boats were ridiculous, so instead we just wandered around, fed ducks, etc.
Restaurants : these are all recommended
Russell House Tavern
Giacomo's (the Columbus location)
Charlie's Sandwich Shoppe
Cafe Vittoria (for espresso)
Thornton's (too busy, staff not very friendly)
Overall, great city. Would come back again!